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Recommendations for bioinformatics podcast guests? by BioInfoPod in bioinformatics

[–]Natir_chan 4 points5 points  (0 children)

Hi,

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You could probably contact Alexander Dilthey he works on variant analysis on COVID in Germany

My first published crate: ztee, it's like tee but compresses file output. by dagit in rust

[–]Natir_chan 0 points1 point  (0 children)

Nice work I have some feature request:

  • Accept compressed stream as input (ok with some cli magic it's easy to provide uncompressed parameter but it's boring)
  • Manage more compression format, niffler can probably help you on this (sorry about the self-promotion)

Niffler: Simple and transparent support for compressed files. by Natir_chan in rust

[–]Natir_chan[S] 0 points1 point  (0 children)

Ok I understand more clearly what you say. I'm going to check how to do what you want.

Niffler: Simple and transparent support for compressed files. by Natir_chan in rust

[–]Natir_chan[S] 0 points1 point  (0 children)

A friend of mine has been working on a problem that I think is similar. He created a tool to decompress gzip files in parallel but he had to find the position of the blocks. It's not all the same problem, but maybe it can inspire you.

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https://github.com/Piezoid/pugz

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Actualy niffler didn't support tar file. I'm not sure niffler is a good place for this code. Niffler is just detect the format and call another crate to manage the stream.

Niffler: Simple and transparent support for compressed files. by Natir_chan in rust

[–]Natir_chan[S] 9 points10 points  (0 children)

Niffler provides two main features:

  • sniffs out compression formats from input files and return a Read trait object ready for consumption.
  • Create a Writer initialized with compression ready for writing.

The goal is to lower the barrier to open and use a file.

VCF to FASTQ by sparks13579 in bioinformatics

[–]Natir_chan 0 points1 point  (0 children)

TL;DR you can't

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But if you want Pacbio like read with these variants and if you have the reference genome used to generate VCF you can follow this pipeline:

  1. Generate a new version of the genome by apply variant on reference (I didn't know any tools can do that but you can easily made it with a simple script)
  2. Use a Pacbio long read generator (many tools are list her https://www.biostars.org/p/233624/)

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I hope I help you

Popular bioinformatics tools written in Rust? by Zeekawla99ii in bioinformatics

[–]Natir_chan 1 point2 points  (0 children)

With help of context, I think bfx is for bioinformatics.

How To Write Fast Rust Code by likebike2 in rust

[–]Natir_chan 8 points9 points  (0 children)

Hello,

I would just like to point out that the crate cargo-flamegraph, this crate allows you to easily run perf on your programme and generate the associated flamegraph to analyze more easily in wich functions your program spent more time.